A penalized maximum likelihood method for estimating epistatic effects of QTL

Heredity

Volumn 95, Issue 1, 2005, Pages 96-104

  Zhang, Y M ^a   Xu, S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Epistatic effect; Marker analysis; Penalized maximum likelihood; Quantitative trait loci

Indexed keywords

EPISTASIS; ESTIMATION METHOD; GENETICS; MAXIMUM LIKELIHOOD ANALYSIS;

ARTICLE; BAYES THEOREM; EVOLUTION; GENETIC EPISTASIS; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL;

BAYES THEOREM; EPISTASIS, GENETIC; EVOLUTION; MODELS, STATISTICAL; QUANTITATIVE TRAIT LOCI;

EID: 22144459429     PISSN: 0018067X     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.hdy.6800702     Document Type: Article

References (27)

1. Akaike H (1973). Second international symposium on information theory. In: Petrox BN, Caski F (eds) Information Theory and an Extension of the Maximum Likelihood Principle. Akademiai Kiado: Budapest. p 267.
2. Balding DJ (2002). Discussion on the meeting on 'statistical modeling and analysis of genetic data'. J R Statist Soc: Ser B 64: 737-775.
3. Boer MP, Braak CJF, Jansen RC (2002). A penalized likelihood method for mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 162: 951-960.
4. Broman KW, Speed TP (2002). A model selection approach for the identification of quantitative trait loci in experiment crosses. J R Statist Soc B 64: 641-656.
5. Cheverud JM, Routman EJ (1995). Epistasis and its contribution to genetic variance components. Genetics 139: 1455-1461.
6. Churchill GA, Doerge RW (1994). Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
7. Cockerham CC (1954). An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 39: 859-882.
8. Falconer DS (1989). Introduction to Quantitative Genetics, 3rd edn. John Wiley and Sons: New York.
9. Gianola D, Perez-Enciso M, Toro MA (2003). On marker-assisted prediction of genetic value: beyond the ridge. Genetics 163: 347-365.
10. Hoerl AE, Kennard RW (1970). Ridge regression: biased estimation for nonorthogonal problems. Technometrics 12: 55-67.
11. Jannink JL, Jansen RC (2001). Mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 157: 445-454.
12. Jansen RC (1994). Controlling the type I and II errors in mapping quantitative trait loci. Genetics 138: 871-881.
13. Kadane JB, Lazar NA (2004). Methods and criteria for model selection. J Am Statist Assoc 99: 279-290.
14. Kao CH, Zeng Z-B (2002). Modeling epistasis of quantitative trait loci using Cockerham's model. Genetics 160: 1243-1261.
15. Kao CH, Zeng Z-B, Teasdale RD (1999). Multiple interval mapping for quantitative trait loci. Genetics 152: 1203-1216.
16. Lander ES, Botstein D (1989). Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
17. Oh C, Ye KQ, He QM, Mendell NR (2003). Locating disease genes using Bayesian variable selection with the Haseman-Elston method. BMC Genet 4(Suppl. 1): S69.
18. Rao SQ, Xu S (1998). Mapping quantitative trait loci for categorical traits in four-way crosses. Heredity 81: 214-224.
19. SAS institute (1999). SAS/IML User's Guide, Version 8. SAS Institute Inc.: Cary.
20. Schwarz G (1978). Estimating the dimension of a model. Ann Statist 6: 461-464.
21. Sen S, Churchill GA (2001). A statistical framework for quantitative trait mapping. Genetics 159: 371-387.
22. Sillanpaa MJ, Corander J (2002). Model choice in gene mapping: what and why. Trends Genet 18: 301-307.
23. Wang H, Zhang Y-M, Li X, Masinde GL, Mohan S, Baylink DJ, Xu S (2005). Bayesian shrinkage estimation of QTL parameters. Genetics (in press), doi:10.1534/genetics.104.039362.
24. Whittaker JC, Thompson R, Denham MG (2000). Marker-assisted selection using ridge regression. Genet Res 75: 249-252.
25. Xu S (2003). Estimating polygenic effects using markers of the entire genome. Genetics 163: 789-801.
26. Xu S, Yi N, Burke D, Galecki A, Miller RA (2003). An EM algorithm for mapping binary disease loci: application to fibrosarcoma in a four-way cross mouse family. Genet Res 82: 127-138.
27. Yi NJ, George V, Allison DB (2003). Stochastic search variable selection for identifying multiple quantitative trait loci. Genetics 164: 1129-1138.